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Status |
Public on Jul 06, 2015 |
Title |
intensive-care unit patient [13_02_2013_H10_394] |
Sample type |
RNA |
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|
Source name |
whole blood
|
Organism |
Homo sapiens |
Characteristics |
gender: female age: 91 pneumonia diagnoses: NA thrombocytopenia: NA endotype_cohort: NA endotype_class: NA mortality_event_28days: NA time_to_event_28days: NA icu_acquired_infection: NA icu_acquired_infection_paired: NA diabetes_mellitus: NA abdominal_sepsis_and_controls: NA
|
Treatment protocol |
PAXgene blood RNA tubes were left at room temperaturee to defrost (4 hours) while mixing by inversion.
|
Growth protocol |
Whole blood was collected in PAXgene blood RNA tubes, mixed by inversion 10X and stored at -80C.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated in accordance with the PAXgene blood RNA isolation (QIAGEN) procedure using the QIAcube workstation.
|
Label |
biotin
|
Label protocol |
100ng total RNA was labeled using standard GeneChip® 3' IVT Express Kit (Affymetrix)
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|
|
Hybridization protocol |
Standard Affymetrix GeneAtlas® Hybridization, Wash, and Stain Kit.
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Scan protocol |
Standard GeneTitan® multi channel instrument.
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Description |
blood gene expression data from healthy subjects and critically-ill patients.
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Data processing |
Raw data scans (.CEL files) were read into the R language and environment for statistical computing (version 2.15.1; R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org/). Pre-processing and quality control was performed by using the Affy package version 1.36.1. Array data were background corrected by Robust Multi-array Average, quantiles-normalized and summarized by medianpolish using the expresso function. The resultant 49,386 probe intensities were filtered by means of a 0.5 variance cutoff using the genefilter method to recover 24,646 expressed probes. The occurrence of non-experimental chip effects was evaluated by means of the Surrogate Variable Analysis (R package version 3.4.0) and corrected by the empirical Bayes method ComBat.
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Submission date |
May 20, 2015 |
Last update date |
Jul 12, 2018 |
Contact name |
Brendon Scicluna |
E-mail(s) |
brendon.scicluna@um.edu.mt
|
Organization name |
University of Malta
|
Street address |
Msida campus
|
City |
Msida |
ZIP/Postal code |
MSD2020 |
Country |
Malta |
|
|
Platform ID |
GPL13667 |
Series (1) |
GSE65682 |
Genome-wide blood transcriptional profiling in critically ill patients - MARS consortium |
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